SELECT 
  cscart_product_prices.product_id, 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_product_prices 
WHERE 
  cscart_product_prices.product_id IN (
    100564, 100494, 100493, 100477, 100251, 
    100248, 100180, 99431, 99373, 93465, 
    100470, 100446, 100405, 100404, 100403, 
    100393, 100392, 100391, 100300, 100247
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00106

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_product_prices range usergroup,product_id,lower_limit,usergroup_id usergroup 9 40 Using where

Result

product_id price
93465 1.69000000
99373 1.69000000
99431 1.69000000
100180 1.69000000
100247 1.69000000
100248 1.69000000
100251 1.69000000
100300 1.69000000
100391 1.69000000
100392 1.69000000
100393 1.69000000
100403 1.69000000
100404 1.69000000
100405 1.69000000
100446 1.69000000
100470 1.69000000
100477 1.69000000
100493 1.69000000
100494 1.69000000
100564 1.69000000